+Open data
-Basic information
Entry | Database: PDB / ID: 7f09 | |||||||||||||||
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Title | Crystal structure of the HLH-Lz domain of human TFE3 | |||||||||||||||
Components | Transcription factor E3 | |||||||||||||||
Keywords | TRANSCRIPTION / Transcription factor E3 / HLH-Lz domain | |||||||||||||||
Function / homology | Function and homology information regulation of osteoclast differentiation / negative regulation of cold-induced thermogenesis / humoral immune response / positive regulation of brown fat cell differentiation / positive regulation of cell adhesion / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / adaptive immune response / protein dimerization activity / transcription cis-regulatory region binding ...regulation of osteoclast differentiation / negative regulation of cold-induced thermogenesis / humoral immune response / positive regulation of brown fat cell differentiation / positive regulation of cell adhesion / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / adaptive immune response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||||||||
Authors | Yang, G. / Li, P. / Liu, Z. / Wu, S. / Zhuang, C. / Qiao, H. / Fang, P. / Wang, J. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Structural basis for the dimerization mechanism of human transcription factor E3. Authors: Yang, G. / Li, P. / Liu, Z. / Wu, S. / Zhuang, C. / Qiao, H. / Zheng, L. / Fang, P. / Lei, C. / Wang, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f09.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f09.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 7f09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f09_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 7f09_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 7f09_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 7f09_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/7f09 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/7f09 | HTTPS FTP |
-Related structure data
Related structure data | 6ku4 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8625.815 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TFE3, BHLHE33 / Production host: Escherichia coli (E. coli) / References: UniProt: P19532 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Zinc Acetate, Zinc Chloride, Bis-Tris pH 7.5, PEG 3350, PEG 2000, PEG 4000 and PEG 5000MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→47.19 Å / Num. obs: 17459 / % possible obs: 94.6 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.041 / Rrim(I) all: 0.058 / Net I/σ(I): 10.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KU4 6ku4 Resolution: 2.6→18.833 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.41 / Phase error: 31.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.48 Å2 / Biso mean: 71.8898 Å2 / Biso min: 30.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→18.833 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -0.5596 Å / Origin y: 4.0699 Å / Origin z: 6.6314 Å
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Refinement TLS group |
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